BtaALTD0005684-2/2 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000010050 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr2:122592730-122594534:+
Coord C1 exon
chr2:122592730-122592774
Coord A exon
chr2:122592775-122592818
Coord C2 exon
chr2:122594481-122594534
Length
44 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTCT
5' ss Score
1.07
3' ss Seq
TCATGATTTTTCTCTCCAAGGGT
3' ss Score
6.84
Exon sequences
Seq C1 exon
GGCCCCCCAGGTTTTCCTGGTGCTGTTGGCTCCCCCGGATTGCCT
Seq A exon
GTAAGAACCTAGCGCTGCTCGACCTCCCCTCCCCTGCCAGCCAG
Seq C2 exon
GGTCTTCAAGGAGAGCGAGGCCTCAGGGGCCTGACGGGAGAGAAGGGGGAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010050-65-67,66-67-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(23.3=100),PF0139113=Collagen=PU(14.3=66.7)
A:
NA
C2:
PF0139113=Collagen=PD(1.7=5.6),PF0139113=Collagen=FE(24.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTTCCTGGTGCTGTTGGCTC
R:
CTCCCCCTTCTCTCCCGTC
Band lengths:
85-129
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development